The complete plastid genome of Amphicarpaea ferruginea Bentham (Leguminosae), a grass species with development and utilization prospect

Abstract We are reporting the complete plastid genome of Amphicarpaea ferruginea, a grass species with development and utilization prospect. The A. ferruginea plastome is 152,531 bp long, with two inverted repeat(IR) regions (25,616 bp each) that separate a large single copy (LSC) region (83,364 bp) and a small single copy (SSC) region (17,935 bp). A total of 130 genes were annotated, including 85 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The phylogenetic tree shows that Amphicarpaea edgeworthii is closely related to Amphicarpaea ferruginea with strong bootstrap support.


Amphicarpaea ferruginea Bentham
is a perennial herbaceous vine belonging to the genus Amphicarpaea in Leguminosae, mainly distributed in Assam state in India, central and southern China, Eastern Himalayas, Myanmar, Nepal, and Thailand (Wu 1995;Kumar and Sane 2003). Due to the unique developmental pattern of the Amphicarpaea species plant, it has become a model plant for the study of plant developmental biology, which has unique significance of breeding (Shan et al. 2009). The morphological characteristics of the Amphicarpaea and Glycine plant are very similar, and they also have a very close relationship of each other (Ohashi and Ohashi 2016). Scientists hope to find the trait genes that control the way Amphicarpaea species develop, allowing soybeans to produce both above-ground and below-ground results to increase yields (Ohashi and Ohashi 2018). In addition, Amphicarpaea species plants are rich in crude protein, calcium and phosphorus, have high forage to value, and are potential high-quality forage resources (Jiang et al. 2013). The seeds contain isoflavones, which have anti-inflammatory, antioxidant, anti-tumor, antibacterial and other effects (Jiang et al. 2007). A. ferruginea is one of the leguminous grass species with development and utilization prospects in the central and southern subtropical regions. In this study, we characterized a complete plastid genome of A. ferruginea and confirmed the phylogenetic relationship of the genus, to provide genetic information for further research on phytogeography, genetic diversity and evolution.
The fresh leaves of A. ferruginea were collected from Nanxi village, Huangshan Town, Yulong County, Yunnan Province, China (coordinates:100 8'59.93 00 E, 26 46'8.02 00 N; altitude: 3103 m). The collection of plant materials complies with the wild plant protection regulations of the people's republic of China and obtain the permission of local authorities on forestry and grassland bureau Yunnan province in China. The voucher specimen (SWFU20210776MFY) was deposited at Herbarium of Southwest Forestry University, China (http:// bbg.swfu.edu.cn/, Yu Xiao, email:yuxiao0215@gmail.com). Total genome DNA was extracted with the Ezup plant genomic DNA preps Kit (Sangon Biotech, Shanghai, China). A total of 3 G raw data from Illumina Hiseq Platform (Illumina, San Diego, CA) were sequenced. Then the raw data was used to assemble the complete chloroplast genome using the software of GetOrganelle (Jin et al. 2020). Annotated using Geneious Prime (Kearse et al. 2012) with reference to the complete plastid genome sequence of A. edgeworthii (NC_057598.1). The complete plastid genome of A. ferruginea was submitted to GenBank with accession number ON050971.
A phylogenetic tree was reconstructed to confirm the phylogenetic location of A. ferruginea. Two species of Cycas debaoensis and Cycas szechuanensis were used as out-groups. All of these 24 complete cp sequences were aligned by the MAFFT version 7 software (Katoh and Standley 2013). A maximum likelihood method for phylogenetic analysis was performed base on GTR þ I þ G model in the RAxML version 8 program with 1000 bootstrap replicates (Darriba et al. 2012;Stamatakis 2014). Phylogenetic analysis results strongly supported that A. ferruginea was sister related to the A. edgeworthii (Figure 1). The complete chloroplast genome sequence of A. ferruginea will provide useful information for further study on genetic diversity and conservation of Amphicarpaea species.
Author contributions X. Y. conceived the study, collected the molecular materials, and drafted the manuscript; Z. N. Z. and H. L. P. analyzed the experimental data. All authors provided comments and final approval.

Disclosure statement
No potential conflict of interest was reported by the author(s).

Data availability statement
The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov under the accession no.ON050971. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA820613, SRR18500621, and SAMN27019003, respectively.